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NCBI C++ ToolKit: src/app/vecscreen/vecscreen_app.cpp Source File

arg_desc->SetUsageContext(

().GetProgramBasename(),

+

arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

,

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arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

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arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

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arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

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arg_desc->AddFlag(

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arg_desc->SetCurrentGroup(

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kDbName(args[

].AsString());

kHtmlOutput = !args[

].AsBoolean();

kTermFlex = args[

].AsInteger();

( !

.End() ) {

query_batch->

(0), kDbName, kTermFlex);

(

argc,

* argv[]

)

#define CATCH_ALL(exit_code)

Standard catch statement for all BLAST command line programs.

#define BLAST_EXIT_SUCCESS

Command line binary exit code: success.

Interface for reading SRA sequences into blast input.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

@ eVecScreen

Vector screening.

Class to constrain the values of an argument to those in between the values specified in the construc...

Class representing a text file containing sequences in fasta format.

Class that centralizes the configuration data for sequences to be converted.

void SetQueryLocalIdMode()

Append query-specific prefix codes to all generated local ids.

Generalized converter from an abstract source of biological sequence data to collections of blast inp...

CRef< objects::CScope > GetScope(size_type i) const

Get the scope containing a query by index.

size_type Size() const

Returns the number of queries found in this query vector.

CConstRef< objects::CSeq_loc > GetQuerySeqLoc(size_type i) const

Get the query Seq-loc for a query by index.

Class whose purpose is to create CScope objects which have data loaders added with different prioriti...

CRef< objects::CScope > NewScope()

Create a new, properly configured CScope.

NCBI C++ Object Manager dependant implementation of IQueryFactory.

virtual void Init()

@inheritDoc

virtual int Run()

@inheritDoc

CVecScreenApp()

@inheritDoc

void FormatResults(CNcbiOstream &out, CRef< blast::CBlastOptionsHandle > vs_opts)

Format the VecScreen results.

@ eEndValue

Sentinel value, not an actual output format.

This class runs vecscreen.

const string kArgOutput

Output file name.

const string kDfltArgQuery

Default value for query sequence input.

const string kArgQuery

Query sequence(s)

const string kArgDb

BLAST database name.

void Print(const CCompactSAMApplication::AlignInfo &ai)

const int kDfltArgOutputFormat

Default value for formatted output type.

const char * kArgOutputFormat

Argument to select formatted output type.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eDiag_Warning

Warning message.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Declares the CRemoteBlast class.

Configuration structure for the CBlastScopeSource.

void OptimizeForWholeLargeSequenceRetrieval(bool value=true)

Configures the BLAST database data loader to optimize the retrieval of *entire* large sequences.

@ eUseBlastDbDataLoader

Use the local BLAST database loader first, if this fails, use the remote BLAST database data loader.

int main(int argc, const char *argv[])

const string kDefaultVectorDb

const TSeqPos kDefaultTerminalFlexibility

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